Contacts of the helix formed by residues 42 - 50 (chain E) in PDB entry 5XTD
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLU 42 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38E ALA 3.1 20.8 + - - +
39E TRP* 2.7 14.6 + - - +
41E ARG* 1.3 78.9 - - - +
43E VAL* 1.3 68.1 + - - +
44E PRO* 3.5 0.4 - - - -
45E ASN* 3.0 33.1 + - + +
46E THR* 2.4 30.9 + - - -
90E LEU* 4.1 6.1 - - + +
93E THR* 3.3 22.5 - - - +
94E ILE* 3.5 32.8 - - + +
201E 8Q1 6.1 0.9 - - - +
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Residues in contact with VAL 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E TRP* 2.9 21.5 + - + +
40E TYR* 4.2 9.0 - - - +
41E ARG 3.1 1.8 - - - -
42E GLU* 1.3 82.9 - - - +
44E PRO* 1.4 65.9 - - + +
46E THR* 3.0 8.2 + - - -
47E VAL* 2.8 40.8 + - + +
56E VAL* 4.0 19.3 - - + +
59E GLY* 4.3 13.0 - - - -
60E ARG* 4.3 8.7 - - + +
63E VAL* 3.6 28.0 - - + -
201E 8Q1 5.0 12.1 - - + -
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Residues in contact with PRO 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E TYR 4.3 4.9 - - - +
41E ARG* 3.3 16.6 - - - +
43E VAL* 1.4 93.7 - - + +
45E ASN* 1.3 59.7 + - - +
47E VAL* 3.0 14.4 + - + +
48E HIS* 2.9 30.7 + - - +
56E VAL* 4.0 7.4 - - + -
60E ARG* 3.7 24.9 - - - +
365J GLU* 5.4 2.5 - - + +
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Residues in contact with ASN 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E ARG 3.7 8.0 + - - +
42E GLU* 3.0 35.8 + - + +
44E PRO* 1.3 79.7 - - - +
46E THR* 1.3 57.5 + - - +
48E HIS* 3.4 3.5 + - - +
49E GLN* 2.9 38.1 + - + +
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Residues in contact with THR 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E GLU* 2.4 40.0 + - - -
43E VAL* 3.0 10.7 + - - -
45E ASN* 1.3 75.3 - - - +
47E VAL* 1.3 65.6 + - + +
48E HIS 3.1 1.9 + - - -
49E GLN* 4.4 4.9 - - - +
50E PHE* 3.3 39.4 + - + -
52E LEU* 3.2 20.3 - - + +
93E THR* 3.4 11.4 + - + +
103E VAL* 4.4 12.3 - - + -
201E 8Q1 5.0 10.1 - - + -
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Residues in contact with VAL 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E VAL* 2.8 31.6 + - + +
44E PRO* 3.0 16.5 + - + +
46E THR* 1.3 76.3 - - - +
48E HIS* 1.3 59.0 + - + +
51E GLN* 3.2 5.2 - - - -
52E LEU* 2.9 49.2 + - + +
54E ILE* 4.2 21.5 - - + +
56E VAL* 3.7 31.4 - - + -
365J GLU* 5.4 11.0 - - + -
366J ILE* 5.8 3.1 - - + +
367J GLU* 5.2 1.1 - - - +
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Residues in contact with HIS 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E PRO 2.9 14.1 + - - +
45E ASN* 4.0 3.8 - - - +
47E VAL* 1.3 78.8 - - - +
49E GLN* 1.3 74.0 + - + +
50E PHE 3.2 1.7 + - - -
51E GLN* 3.3 16.4 + - - +
363J SER* 2.9 55.8 + - - -
364J ALA* 3.8 4.5 + - - -
365J GLU* 3.4 32.7 + - + +
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Residues in contact with GLN 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E ASN* 2.9 25.5 + - + +
46E THR* 4.3 2.2 - - - +
48E HIS* 1.3 84.4 - - + +
50E PHE* 1.3 82.0 + - + +
51E GLN* 4.9 2.3 - - - +
96E VAL* 3.2 34.7 - - + +
43j PRO 5.5 2.6 + - - +
44j MET 3.5 21.1 + - - +
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Residues in contact with PHE 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46E THR* 3.3 29.4 + - + -
49E GLN* 1.3 99.9 - - + +
51E GLN* 1.3 63.6 + - - +
52E LEU* 3.4 13.4 + - + -
93E THR* 4.0 25.1 - - + -
96E VAL* 3.6 23.6 - - + -
97E TRP 4.0 16.6 - - - -
98E LYS* 5.4 1.1 - - + -
99E GLN 5.0 2.0 - - - -
100E ARG* 2.8 53.0 + - + +
103E VAL* 3.4 33.2 - - + -
42j ASP* 4.9 13.9 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il